In most cases, the conflicts that arise from the daily encounters people have between Torah and science are based on misunderstandings.
Often it is a mistake about Torah, and people end up trying to defend the sheer nonsense that they, for some strange reason, believe is Yiddishkeit.
These people find they cannot continue with their religion because they think it is ridiculous.
In fact, their "religion" is indeed ridiculous.
When I was a young man, I met someone in Israel who was then a very important political personality (interestingly, he was son of a famous rabbi, a member of the Mo'etzel Gedolei HaTorah in Poland).
We were talking, and he asked me, "Where does God put his legs?"
For a moment I thought he was joking, but he wasn't.
When I tried to tell him that, as far as I knew, God has no legs, he told me I did not know what I was talking about, because his father truly believed that God has legs!
I tried to remonstrate.
I opened the Siddur and showed him that not only do we not believe that, but we should not: it is forbidden.
He ended the conversation by telling me that he was very friendly with the rosh yeshivah of Mir, and that he would warn him that there was a person in Jerusalem who should be destroyed.
–Rabbi Adin Steinsaltz
From as essay "Where Do Science and Torah Clash" by Rabbi Adin Steinsaltz